FMO DATABASE

FMODB ID: LZ249

Calculation Name: 3LOD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LOD

Chain ID: A

ChEMBL ID:

UniProt ID: A6T8Z3

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	145
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1322925.183185
FMO2-HF: Nuclear repulsion	1266357.104345
FMO2-HF: Total energy	-56568.07884
FMO2-MP2: Total energy	-56731.814058

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:-1:ASN)

Summations of interaction energy for fragment #1(A:-1:ASN)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-34.332	-27.989	8.4	-6.156	-8.585	0.029

Interaction energy analysis for fragmet #1(A:-1:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.050 / q_NPA : 0.027

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	1	MET	0	-0.042	-0.023	1.936	-12.768	-10.368	6.727	-4.438	-4.690	0.039
4	A	2	TYR	0	0.005	0.004	2.648	-6.781	-5.539	1.174	-0.453	-1.963	0.003
5	A	3	THR	0	-0.003	0.004	5.689	0.424	0.424	0.000	0.000	0.000	0.000
6	A	4	ILE	0	-0.012	-0.018	9.233	-0.382	-0.382	0.000	0.000	0.000	0.000
7	A	5	THR	0	-0.031	-0.012	12.418	0.093	0.093	0.000	0.000	0.000	0.000
8	A	6	ASP	-1	-0.784	-0.882	16.003	0.125	0.125	0.000	0.000	0.000	0.000
9	A	7	ILE	0	-0.030	-0.004	18.037	-0.001	-0.001	0.000	0.000	0.000	0.000
10	A	8	ALA	0	0.037	0.028	20.714	0.008	0.008	0.000	0.000	0.000	0.000
11	A	9	PRO	0	0.025	0.004	23.403	-0.028	-0.028	0.000	0.000	0.000	0.000
12	A	10	THR	0	-0.006	-0.022	25.295	-0.018	-0.018	0.000	0.000	0.000	0.000
13	A	11	ASP	-1	-0.890	-0.934	21.168	-0.156	-0.156	0.000	0.000	0.000	0.000
14	A	12	ALA	0	0.033	0.011	22.894	-0.027	-0.027	0.000	0.000	0.000	0.000
15	A	13	GLU	-1	-0.790	-0.876	16.056	-0.366	-0.366	0.000	0.000	0.000	0.000
16	A	14	PHE	0	0.005	0.007	19.274	-0.057	-0.057	0.000	0.000	0.000	0.000
17	A	15	ILE	0	0.001	-0.006	20.643	-0.034	-0.034	0.000	0.000	0.000	0.000
18	A	16	ALA	0	-0.011	0.003	20.056	-0.017	-0.017	0.000	0.000	0.000	0.000
19	A	17	LEU	0	0.004	-0.003	15.227	-0.047	-0.047	0.000	0.000	0.000	0.000
20	A	18	ILE	0	-0.022	-0.014	19.225	-0.029	-0.029	0.000	0.000	0.000	0.000
21	A	19	ALA	0	0.000	0.008	22.483	0.004	0.004	0.000	0.000	0.000	0.000
22	A	20	ALA	0	-0.010	-0.004	19.393	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	21	LEU	0	-0.050	-0.026	20.604	-0.026	-0.026	0.000	0.000	0.000	0.000
24	A	22	ASP	-1	-0.769	-0.857	21.800	-0.327	-0.327	0.000	0.000	0.000	0.000
25	A	23	ALA	0	-0.010	0.002	23.646	0.013	0.013	0.000	0.000	0.000	0.000
26	A	24	TRP	0	-0.051	-0.014	20.344	-0.032	-0.032	0.000	0.000	0.000	0.000
27	A	25	GLN	0	-0.036	-0.037	23.765	0.011	0.011	0.000	0.000	0.000	0.000
28	A	26	GLU	-1	-0.906	-0.927	26.003	-0.281	-0.281	0.000	0.000	0.000	0.000
29	A	27	THR	0	-0.171	-0.090	26.016	0.019	0.019	0.000	0.000	0.000	0.000
30	A	37	LEU	0	0.055	0.010	28.108	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	38	ASP	-1	-0.896	-0.944	30.136	-0.119	-0.119	0.000	0.000	0.000	0.000
32	A	39	LEU	0	0.029	0.008	25.530	0.012	0.012	0.000	0.000	0.000	0.000
33	A	40	SER	0	-0.080	-0.042	29.324	0.019	0.019	0.000	0.000	0.000	0.000
34	A	41	GLN	0	-0.041	-0.023	30.395	0.005	0.005	0.000	0.000	0.000	0.000
35	A	42	LEU	0	0.008	0.015	31.005	0.010	0.010	0.000	0.000	0.000	0.000
36	A	43	PRO	0	0.025	0.020	33.101	0.005	0.005	0.000	0.000	0.000	0.000
37	A	44	PRO	0	0.055	0.021	30.032	0.005	0.005	0.000	0.000	0.000	0.000
38	A	45	GLN	0	0.042	0.024	29.853	0.000	0.000	0.000	0.000	0.000	0.000
39	A	46	THR	0	-0.047	-0.026	30.958	0.009	0.009	0.000	0.000	0.000	0.000
40	A	47	VAL	0	-0.015	0.002	26.140	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	48	ILE	0	-0.007	0.009	21.904	0.027	0.027	0.000	0.000	0.000	0.000
42	A	49	ALA	0	0.012	-0.002	21.845	-0.036	-0.036	0.000	0.000	0.000	0.000
43	A	50	LEU	0	-0.013	-0.001	16.554	0.049	0.049	0.000	0.000	0.000	0.000
44	A	51	ALA	0	0.031	0.004	14.982	-0.100	-0.100	0.000	0.000	0.000	0.000
45	A	52	ILE	0	-0.030	-0.012	8.906	0.172	0.172	0.000	0.000	0.000	0.000
46	A	53	ARG	1	0.774	0.847	9.979	-0.086	-0.086	0.000	0.000	0.000	0.000
47	A	54	SER	0	-0.001	-0.030	6.258	0.549	0.549	0.000	0.000	0.000	0.000
48	A	55	PRO	0	-0.034	-0.030	3.679	0.250	0.474	0.000	-0.032	-0.191	0.000
49	A	56	GLN	0	-0.009	-0.004	6.731	-0.023	-0.023	0.000	0.000	0.000	0.000
50	A	57	GLY	0	0.022	0.024	9.477	0.149	0.149	0.000	0.000	0.000	0.000
51	A	58	GLU	-1	-0.817	-0.871	9.798	-1.623	-1.623	0.000	0.000	0.000	0.000
52	A	59	ALA	0	0.008	0.009	10.957	-0.055	-0.055	0.000	0.000	0.000	0.000
53	A	60	VAL	0	-0.023	-0.005	8.350	-0.124	-0.124	0.000	0.000	0.000	0.000
54	A	61	GLY	0	0.007	-0.010	11.550	-0.188	-0.188	0.000	0.000	0.000	0.000
55	A	62	CYS	0	-0.030	0.002	13.616	0.132	0.132	0.000	0.000	0.000	0.000
56	A	63	GLY	0	0.025	0.020	16.620	-0.072	-0.072	0.000	0.000	0.000	0.000
57	A	64	ALA	0	-0.003	0.005	19.540	0.053	0.053	0.000	0.000	0.000	0.000
58	A	65	ILE	0	-0.023	-0.009	22.636	-0.019	-0.019	0.000	0.000	0.000	0.000
59	A	66	VAL	0	0.010	0.019	25.357	0.014	0.014	0.000	0.000	0.000	0.000
60	A	67	LEU	0	-0.003	-0.017	27.731	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	68	SER	0	-0.038	-0.029	30.920	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	69	GLU	-1	-0.890	-0.955	34.629	0.001	0.001	0.000	0.000	0.000	0.000
63	A	70	GLU	-1	-0.938	-0.961	37.233	0.011	0.011	0.000	0.000	0.000	0.000
64	A	71	GLY	0	0.020	0.017	33.488	0.001	0.001	0.000	0.000	0.000	0.000
65	A	72	PHE	0	0.013	0.001	31.594	0.002	0.002	0.000	0.000	0.000	0.000
66	A	73	GLY	0	0.038	0.018	28.984	0.006	0.006	0.000	0.000	0.000	0.000
67	A	74	GLU	-1	-0.823	-0.872	28.095	-0.153	-0.153	0.000	0.000	0.000	0.000
68	A	75	MET	0	-0.012	-0.002	20.285	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	76	LYS	1	0.851	0.904	24.328	0.131	0.131	0.000	0.000	0.000	0.000
70	A	77	ARG	1	0.792	0.852	23.194	0.299	0.299	0.000	0.000	0.000	0.000
71	A	78	VAL	0	0.026	0.018	17.399	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	79	TYR	0	-0.002	-0.019	15.852	-0.026	-0.026	0.000	0.000	0.000	0.000
73	A	80	ILE	0	0.005	-0.003	10.722	0.004	0.004	0.000	0.000	0.000	0.000
74	A	81	ASP	-1	-0.742	-0.851	12.079	-1.346	-1.346	0.000	0.000	0.000	0.000
75	A	82	PRO	0	-0.041	-0.037	11.742	-0.336	-0.336	0.000	0.000	0.000	0.000
76	A	83	GLN	0	-0.058	-0.026	10.635	-0.153	-0.153	0.000	0.000	0.000	0.000
77	A	84	HIS	0	0.043	0.044	7.239	-1.421	-1.421	0.000	0.000	0.000	0.000
78	A	85	ARG	1	0.858	0.931	7.452	0.905	0.905	0.000	0.000	0.000	0.000
79	A	86	GLY	0	0.008	0.000	7.822	-0.529	-0.529	0.000	0.000	0.000	0.000
80	A	87	GLN	0	-0.049	-0.026	2.732	-7.527	-5.063	0.500	-1.220	-1.743	-0.013
81	A	88	GLN	0	0.002	-0.011	4.651	-0.895	-0.882	-0.001	-0.013	0.002	0.000
82	A	89	LEU	0	0.000	0.007	5.583	1.033	1.033	0.000	0.000	0.000	0.000
83	A	90	GLY	0	0.028	0.020	8.639	0.409	0.409	0.000	0.000	0.000	0.000
84	A	91	GLU	-1	-0.750	-0.868	10.094	-0.966	-0.966	0.000	0.000	0.000	0.000
85	A	92	LYS	1	0.827	0.916	6.783	-2.823	-2.823	0.000	0.000	0.000	0.000
86	A	93	LEU	0	0.022	0.005	11.133	0.184	0.184	0.000	0.000	0.000	0.000
87	A	94	LEU	0	0.006	0.010	13.891	0.068	0.068	0.000	0.000	0.000	0.000
88	A	95	ALA	0	0.014	0.003	13.971	0.054	0.054	0.000	0.000	0.000	0.000
89	A	96	ALA	0	-0.006	-0.002	14.417	0.049	0.049	0.000	0.000	0.000	0.000
90	A	97	LEU	0	0.005	-0.004	16.440	0.007	0.007	0.000	0.000	0.000	0.000
91	A	98	GLU	-1	-0.727	-0.833	19.294	0.024	0.024	0.000	0.000	0.000	0.000
92	A	99	ALA	0	-0.054	-0.019	18.888	0.012	0.012	0.000	0.000	0.000	0.000
93	A	100	LYS	1	0.830	0.888	19.686	-0.215	-0.215	0.000	0.000	0.000	0.000
94	A	101	ALA	0	0.020	0.013	22.323	-0.014	-0.014	0.000	0.000	0.000	0.000
95	A	102	ARG	1	0.835	0.904	20.482	-0.144	-0.144	0.000	0.000	0.000	0.000
96	A	103	GLN	0	-0.068	-0.031	21.256	-0.015	-0.015	0.000	0.000	0.000	0.000
97	A	104	ARG	1	0.813	0.899	26.337	-0.079	-0.079	0.000	0.000	0.000	0.000
98	A	105	ASP	-1	-0.898	-0.932	29.003	0.098	0.098	0.000	0.000	0.000	0.000
99	A	106	CYS	0	-0.106	-0.033	27.539	-0.019	-0.019	0.000	0.000	0.000	0.000
100	A	107	HIS	0	0.033	0.012	28.210	0.012	0.012	0.000	0.000	0.000	0.000
101	A	108	THR	0	-0.050	-0.034	28.346	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	109	LEU	0	-0.008	0.009	23.271	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	110	ARG	1	0.831	0.899	26.962	0.051	0.051	0.000	0.000	0.000	0.000
104	A	111	LEU	0	-0.013	0.004	22.579	0.000	0.000	0.000	0.000	0.000	0.000
105	A	112	GLU	-1	-0.832	-0.926	26.622	-0.228	-0.228	0.000	0.000	0.000	0.000
106	A	113	THR	0	-0.044	-0.003	22.684	-0.032	-0.032	0.000	0.000	0.000	0.000
107	A	114	GLY	0	0.108	0.062	26.138	0.015	0.015	0.000	0.000	0.000	0.000
108	A	115	ILE	0	-0.010	-0.024	26.107	-0.032	-0.032	0.000	0.000	0.000	0.000
109	A	116	HIS	0	0.003	0.007	25.827	-0.022	-0.022	0.000	0.000	0.000	0.000
110	A	117	GLN	0	-0.032	-0.012	22.183	-0.022	-0.022	0.000	0.000	0.000	0.000
111	A	118	HIS	0	0.036	0.011	21.300	-0.025	-0.025	0.000	0.000	0.000	0.000
112	A	119	ALA	0	-0.010	-0.008	16.079	0.004	0.004	0.000	0.000	0.000	0.000
113	A	120	ALA	0	0.004	0.011	16.885	-0.038	-0.038	0.000	0.000	0.000	0.000
114	A	121	ILE	0	0.077	0.042	18.760	0.032	0.032	0.000	0.000	0.000	0.000
115	A	122	ALA	0	0.009	0.016	17.608	0.042	0.042	0.000	0.000	0.000	0.000
116	A	123	LEU	0	-0.073	-0.030	13.312	0.006	0.006	0.000	0.000	0.000	0.000
117	A	124	TYR	0	0.080	0.030	16.333	0.043	0.043	0.000	0.000	0.000	0.000
118	A	125	THR	0	-0.003	-0.013	19.461	0.059	0.059	0.000	0.000	0.000	0.000
119	A	126	ARG	1	0.754	0.848	11.296	0.846	0.846	0.000	0.000	0.000	0.000
120	A	127	ASN	0	-0.063	-0.033	14.162	0.089	0.089	0.000	0.000	0.000	0.000
121	A	128	GLY	0	0.018	0.012	17.958	0.051	0.051	0.000	0.000	0.000	0.000
122	A	129	TYR	0	-0.043	-0.031	20.082	0.017	0.017	0.000	0.000	0.000	0.000
123	A	130	GLN	0	-0.025	-0.018	23.588	-0.020	-0.020	0.000	0.000	0.000	0.000
124	A	131	THR	0	0.021	0.012	26.642	0.000	0.000	0.000	0.000	0.000	0.000
125	A	132	ARG	1	0.760	0.870	28.797	0.108	0.108	0.000	0.000	0.000	0.000
126	A	133	CYS	0	0.013	-0.004	32.161	-0.011	-0.011	0.000	0.000	0.000	0.000
127	A	134	ALA	0	0.053	0.034	33.930	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	135	PHE	0	-0.040	-0.032	29.954	0.013	0.013	0.000	0.000	0.000	0.000
129	A	136	ALA	0	0.045	0.041	35.482	-0.008	-0.008	0.000	0.000	0.000	0.000
130	A	137	PRO	0	0.000	-0.007	34.213	0.005	0.005	0.000	0.000	0.000	0.000
131	A	138	TYR	0	-0.021	-0.039	30.527	-0.004	-0.004	0.000	0.000	0.000	0.000
132	A	139	GLN	0	0.028	0.008	36.481	0.007	0.007	0.000	0.000	0.000	0.000
133	A	140	PRO	0	-0.054	-0.057	36.860	-0.009	-0.009	0.000	0.000	0.000	0.000
134	A	141	ASP	-1	-0.826	-0.916	35.009	-0.166	-0.166	0.000	0.000	0.000	0.000
135	A	142	PRO	0	-0.166	-0.042	34.343	-0.011	-0.011	0.000	0.000	0.000	0.000
136	A	143	LEU	0	-0.007	-0.001	31.833	0.007	0.007	0.000	0.000	0.000	0.000
137	A	144	SER	0	0.087	0.005	30.679	-0.020	-0.020	0.000	0.000	0.000	0.000
138	A	145	VAL	0	-0.084	-0.040	26.994	0.011	0.011	0.000	0.000	0.000	0.000
139	A	146	PHE	0	0.004	0.024	27.883	-0.009	-0.009	0.000	0.000	0.000	0.000
140	A	147	MET	0	-0.046	-0.033	23.099	-0.010	-0.010	0.000	0.000	0.000	0.000
141	A	148	GLU	-1	-0.786	-0.862	27.042	-0.058	-0.058	0.000	0.000	0.000	0.000
142	A	149	LYS	1	0.843	0.901	19.921	0.008	0.008	0.000	0.000	0.000	0.000
143	A	150	PRO	0	0.000	0.021	26.096	0.006	0.006	0.000	0.000	0.000	0.000
144	A	151	LEU	0	-0.040	-0.031	23.111	0.005	0.005	0.000	0.000	0.000	0.000
145	A	152	PHE	0	0.006	0.017	25.231	0.036	0.036	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-1:ASN)